lumiR                  package:lumi                  R Documentation

_R_e_a_d _i_n _I_l_l_u_m_i_n_a _e_x_p_r_e_s_s_i_o_n _d_a_t_a

_D_e_s_c_r_i_p_t_i_o_n:

     Read in Illumina expression data. We assume the data was saved in
     a comma or tab separated text file.

_U_s_a_g_e:

     lumiR(fileName, sep = NULL, detectionTh = 0.01, na.rm = TRUE, lib = NULL, dec='.', parseColumnName=TRUE, 
     columnNameGrepPattern = list(exprs='AVG_SIGNAL', se.exprs='BEAD_STD', detection='Detection', beadNum='Avg_NBEADS'))

_A_r_g_u_m_e_n_t_s:

fileName: fileName of the data file 

     sep: the separation character used in the text file.  

detectionTh: the p-value threshold of determining detectability of the
          expression. The detection value less than the detectionTh is
          claimed as detectable. 

   na.rm: determine whether to remove NA 

     lib: the annotation library used by 'addNuId2lumi'  

     dec: the character used in the file for decimal points.

parseColumnName: determine whether to parse the column names and
          retrieve the sample information (assume the naming of the
          column names are meaningful.) 

columnNameGrepPattern: the string grep patterns used to determine the
          slot corresponding columns.

_D_e_t_a_i_l_s:

     The function can automatically determine the separation character
     if it is Tab or comma. Otherwise, the user should specify the
     separator manually. If the annotation library is provided, the
     Illumina Id will be replaced with nuID, which is used as the index
     Id for the lumi annotation packages.

     The parameter "columnNameGrepPattern" is designed for some
     advanced users. It defines the string grep patterns used to
     determine the slot corresponding columns. For example, for the
     "exprs" slot in LumiBatch object, it is composed of the columns
     whose name includes "AVG_SIGNAL". In some cases, the user may not
     want to read the "detection" and "beadNum" related columns to save
     memory. The user can set the "detection" and "beadNum" as NA in
     "columnNameGrepPattern". If the 'se.exprs' is set as NA or the
     corresponding columns are not available, then lumiR will create a
     ExpressionSet object instead of LumiBatch object.

     Current version of lumiR can adaptively read the output of
     BeadStudio Verson 1 and 3. The format Version 3 made quite a few
     changes comparing with previous versions. One change is the
     detection value. It was called detectable when the detection value
     is close to one for Version 1 format. However, the detection value
     became a p-value in the Version 3. As a result, the detectionTh is
     automatically changed based on the version. The detectionTh 0.01
     for the Version 3 will be changed as the detectionTh 0.99 for
     Version 1. Another big change is that Version 3 separately output
     the control probe (gene) information and a "Samples Table". As a
     result, the controlData slot in LumiBatch class was added to keep
     the control probe (gene) information, and a QC slot to keep the
     quality control information, including the "Sample Table" output
     by BeadStudio version 3.

_V_a_l_u_e:

     return a LumiBatch object

_A_u_t_h_o_r(_s):

     Simon Lin, Pan Du

_S_e_e _A_l_s_o:

     'LumiBatch', 'addNuId2lumi'

_E_x_a_m_p_l_e_s:

     ## specify the file name
     # fileName <- 'Barnes_gene_profile.txt' # Not Run
     ## load the data
     # x.lumi <- lumiR(fileName)

     ## load the data with empty detection and beadNum slots
     # x.lumi <- lumiR(fileName, columnNameGrepPattern=list(detection=NA, beadNum=NA))

